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rh_tsp_map 3.0：具有更高速度和质量控制的端到端辐射杂种图谱绘制

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control.

作者信息

Schäffer Alejandro A, Rice Edward Stallknecht, Cook William, Agarwala Richa

机构信息

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

出版信息

Bioinformatics. 2007 May 1;23(9):1156-8. doi: 10.1093/bioinformatics/btm077. Epub 2007 Mar 1.

DOI:10.1093/bioinformatics/btm077
PMID:17332018
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2266093/
Abstract

UNLABELLED

rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps.

AVAILABILITY

rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm

摘要

未标注

rh_tsp_map是一个用于计算辐射杂种（RH）图谱以及整合物理图谱和遗传图谱的软件包。它通过将核心映射实例简化为旅行商问题（TSP）并使用对CONCORDE软件包的一种修改来解决TSP实例，从而解决这些核心映射实例。我们展示了在rh_tsp_map初始版本1.0和当前版本3.0之间添加的一些功能，重点强调了许多步骤的自动化以及为发现输入数据问题而添加的各种检查。对改进后的输入数据进行迭代，然后快速重新计算图谱，可提高最终图谱的质量。

可用性

rh_tsp_map的源代码和包括教程在内的文档可在ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz获取。为RH映射修改后的CONCORDE可在目录http://www.isye.gatech.edu/~wcook/rh/中获取。CONCORDE所需的QSopt库可在http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm获取

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